# periodic boundary conditions along all three dimensions boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.165199972689152*${_u_distance} variable latticeconst_converted equal 3.165199972689152*1 lattice bcc ${latticeconst_converted} lattice bcc 3.16519997268915 Lattice spacing in x,y,z = 3.1652 3.1652 3.1652 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.652 31.652 31.652) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.652 31.652 31.652) create_atoms CPU = 0.000 seconds variable mass_converted equal 183.84*${_u_mass} variable mass_converted equal 183.84*1 kim interactions W #=== BEGIN kim interactions ================================== pair_style kim EAM_MagneticCubic_DerletNguyenDudarev_2007_W__MO_195478838873_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * W #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 183.84 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31710.5270189675 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*1*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31710.5270189675*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31710.5270189675 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 273.15 17 mom yes rot yes # set NPT ensemble for all atoms fix ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/1 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/1 variable T_metal equal temp/${_u_temperature} variable T_metal equal temp/1 variable V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*1*${_u_distance}) variable V_metal equal vol/(1*1*1) variable P_metal equal press/${_u_pressure} variable P_metal equal press/1 fix avgmyTemp all ave/time 5 20 100 v_T_metal ave running start 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # extract fix quantities into variables so they can be used in if-else logic later. variable T equal f_avgmyTemp variable P equal f_avgmyPress variable V equal f_avgmyVol # set error bounds for temperature and pressure in original metal units (K and bar) variable T_low equal "273.15 - 1.0" variable T_up equal "273.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # print to logfile every 1000 timesteps thermo_style custom step etotal v_etotal_metal pe v_pe_metal temp v_T_metal vol v_V_metal press v_P_metal thermo 1000 # Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check # whether the temperature and pressure have converged. If yes, break. label top variable a loop 2000 run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_195478838873_002#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17729.421 -17729.421 -17800 -17800 273.15 273.15 31710.527 31710.527 2377.3411 2377.3411 1000 -17661.955 -17661.955 -17732.007 -17732.007 271.10954 271.10954 31721.952 31721.952 -945.57232 -945.57232 Loop time of 2.25359 on 1 procs for 1000 steps with 2000 atoms Performance: 38.339 ns/day, 0.626 hours/ns, 443.737 timesteps/s, 887.475 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1766 | 2.1766 | 2.1766 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010814 | 0.010814 | 0.010814 | 0.0 | 0.48 Output | 0.00014307 | 0.00014307 | 0.00014307 | 0.0 | 0.01 Modify | 0.06014 | 0.06014 | 0.06014 | 0.0 | 2.67 Other | | 0.005874 | | | 0.26 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116000 ave 116000 max 116000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116000 Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 272.563756477943, Press = 53.544308918149 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17661.955 -17661.955 -17732.007 -17732.007 271.10954 271.10954 31721.952 31721.952 -945.57232 -945.57232 2000 -17665.513 -17665.513 -17735.436 -17735.436 270.61134 270.61134 31720.839 31720.839 -84.23236 -84.23236 Loop time of 2.89737 on 1 procs for 1000 steps with 2000 atoms Performance: 29.820 ns/day, 0.805 hours/ns, 345.140 timesteps/s, 690.281 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.815 | 2.815 | 2.815 | 0.0 | 97.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011 | 0.011 | 0.011 | 0.0 | 0.38 Output | 0.00015274 | 0.00015274 | 0.00015274 | 0.0 | 0.01 Modify | 0.06504 | 0.06504 | 0.06504 | 0.0 | 2.24 Other | | 0.006176 | | | 0.21 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2983 ave 2983 max 2983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117454 ave 117454 max 117454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117454 Ave neighs/atom = 58.727 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 272.819032805498, Press = 11.7897099735383 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17665.513 -17665.513 -17735.436 -17735.436 270.61134 270.61134 31720.839 31720.839 -84.23236 -84.23236 3000 -17658.408 -17658.408 -17728.444 -17728.444 271.04785 271.04785 31644.44 31644.44 8982.9093 8982.9093 Loop time of 3.08088 on 1 procs for 1000 steps with 2000 atoms Performance: 28.044 ns/day, 0.856 hours/ns, 324.582 timesteps/s, 649.164 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9949 | 2.9949 | 2.9949 | 0.0 | 97.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01169 | 0.01169 | 0.01169 | 0.0 | 0.38 Output | 0.0001245 | 0.0001245 | 0.0001245 | 0.0 | 0.00 Modify | 0.067938 | 0.067938 | 0.067938 | 0.0 | 2.21 Other | | 0.006197 | | | 0.20 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3021 ave 3021 max 3021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117266 ave 117266 max 117266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117266 Ave neighs/atom = 58.633 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 272.753106828376, Press = 14.5190481041199 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -17658.408 -17658.408 -17728.444 -17728.444 271.04785 271.04785 31644.44 31644.44 8982.9093 8982.9093 4000 -17660.11 -17660.11 -17731.373 -17731.373 275.79705 275.79705 31726.783 31726.783 -1522.0389 -1522.0389 Loop time of 3.35719 on 1 procs for 1000 steps with 2000 atoms Performance: 25.736 ns/day, 0.933 hours/ns, 297.868 timesteps/s, 595.736 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.264 | 3.264 | 3.264 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012709 | 0.012709 | 0.012709 | 0.0 | 0.38 Output | 6.1204e-05 | 6.1204e-05 | 6.1204e-05 | 0.0 | 0.00 Modify | 0.073586 | 0.073586 | 0.073586 | 0.0 | 2.19 Other | | 0.006818 | | | 0.20 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3042 ave 3042 max 3042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117730 ave 117730 max 117730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117730 Ave neighs/atom = 58.865 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 31716.8258396812 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0